[Avida-SVN] r1727 - in development/tests/analyze_detail_all: . config
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Fri Jun 29 09:47:05 PDT 2007
Author: blwalker
Date: 2007-06-29 12:47:05 -0400 (Fri, 29 Jun 2007)
New Revision: 1727
Removed:
development/tests/analyze_detail_all/expected/
Modified:
development/tests/analyze_detail_all/config/analyze.cfg
development/tests/analyze_detail_all/config/avida.cfg
development/tests/analyze_detail_all/test_list
Log:
Cleaning up some stuff in the analyze_detail_all test: most importantly, gave it a constant seed, which requires regenerating the expected results.
Note that this test is not long but is *marked* long, because some code change -- either in analyze or in analyze scripting -- since r1719 causes it to hang in later revisions. Marking it long effecively stops it from causing the whole testing process to hang.
Modified: development/tests/analyze_detail_all/config/analyze.cfg
===================================================================
--- development/tests/analyze_detail_all/config/analyze.cfg 2007-06-28 21:51:13 UTC (rev 1726)
+++ development/tests/analyze_detail_all/config/analyze.cfg 2007-06-29 16:47:05 UTC (rev 1727)
@@ -1,34 +1,34 @@
+##################################################################
+#
+# This analyze file is for testing detail output options. It
+# outputs them all except those specific to sexual genotypes and
+# those which force landscaping, in both .dat and .html format.
+#
+# blw
+##################################################################
-############################################################################
-# This analyze file is meant to test all the possible detail output options.
-# In fact, it does not.
-# It does not test options pertaining to sexual organisms only, and it
-# does not test options that force landscaping.
-# Everything else should be covered, in both .dat and .html format
-############################################################################
-
VERBOSE
-# files are from one of my nature03update runs (s100)
+# .pop files are taken from one of my nature03update runs, seed 100
LOAD data/detail-5000.pop
LOAD data/historic-50000.pop
-# options available immediately after data has been loaded in
+# output options available without any manipulation
DETAIL detail-initial.dat id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list
DETAIL detail-initial.html id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list
-# options available after a recalculate
+# output options available after RECALCULATE
RECALCULATE
DETAIL detail-recalc.dat id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary
DETAIL detail-recalc.html id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary
-# options available after a find_lineage and recalculate
+# output options available after FIND_LINEAGE and RECALCULATE
FIND_LINEAGE
RECALCULATE
DETAIL detail-lineage.dat id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary parent_dist ancestor_dist comp_merit_ratio efficiency_ratio fitness_ratio parent_muts
DETAIL detail-lineage.html id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary parent_dist ancestor_dist comp_merit_ratio efficiency_ratio fitness_ratio parent_muts html.sequence
-# options available after find_lineage, recalculate, and align
+# output options available after ALIGN
ALIGN
DETAIL detail-aligned.dat id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary parent_dist ancestor_dist comp_merit_ratio efficiency_ratio fitness_ratio parent_muts alignment alignment_executed_flags
-DETAIL detail-aligned.html id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary parent_dist ancestor_dist comp_merit_ratio efficiency_ratio fitness_ratio parent_muts html.sequence alignment alignment_executed_flags
\ No newline at end of file
+DETAIL detail-aligned.html id parent_id num_cpus total_cpus length update_born update_dead depth sequence task_list viable copy_length exe_length merit comp_merit gest_time efficiency fitness div_type executed_flags task_order task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 task.0:binary task.1:binary task.2:binary task.3:binary task.4:binary task.5:binary task.6:binary task.7:binary task.8:binary parent_dist ancestor_dist comp_merit_ratio efficiency_ratio fitness_ratio parent_muts html.sequence alignment alignment_executed_flags
Modified: development/tests/analyze_detail_all/config/avida.cfg
===================================================================
--- development/tests/analyze_detail_all/config/avida.cfg 2007-06-28 21:51:13 UTC (rev 1726)
+++ development/tests/analyze_detail_all/config/avida.cfg 2007-06-29 16:47:05 UTC (rev 1727)
@@ -17,14 +17,16 @@
### ARCH_GROUP ###
# Architecture Variables
WORLD_X 60 # Width of the Avida world
-WORLD_Y 60 # Height of the Avida world
+WORLD_Y 60 # Height of the Avida world
WORLD_GEOMETRY 2 # 1 = Bounded Grid
# 2 = Torus
-NUM_DEMES 0 # Number of independed groups in the population; 0=off
+ # 3 = Clique
RANDOM_SEED 0 # Random number seed (0 for based on time)
HARDWARE_TYPE 0 # 0 = Original CPUs
# 1 = New SMT CPUs
# 2 = Transitional SMT
+ # 3 = Experimental CPU
+ # 4 = Gene Expression CPU
### CONFIG_FILE_GROUP ###
# Configuration Files
@@ -35,6 +37,20 @@
ENVIRONMENT_FILE environment.cfg # File that describes the environment
START_CREATURE default-classic.org # Organism to seed the soup
+### DEME_GROUP ###
+# Demes and Germlines
+NUM_DEMES 1 # Number of independent groups in the population.
+DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline; 0=off
+DEMES_HAVE_MERIT 0 # Whether demes have merit; 0=no
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication.
+GERMLINE_REPLACES_SOURCE 0 # Whether the source germline is updated
+ # on replication; 0=no.
+GERMLINE_RANDOM_PLACEMENT 0 # Whether the seed for a germline is placed
+ # randomly within the deme; 0=no.
+MAX_DEME_AGE 500 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+
### REPRODUCTION_GROUP ###
# Birth and Death
BIRTH_METHOD 0 # Which organism should be replaced on birth?
@@ -47,7 +63,10 @@
# 6 = Random within deme
# 7 = Organism faced by parent
# 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
DEATH_METHOD 2 # 0 = Never die of old age.
# 1 = Die when inst executed = AGE_LIMIT (+deviation)
# 2 = Die when inst executed = length*AGE_LIMIT (+dev)
@@ -62,6 +81,8 @@
# (after the divide, we have 2 children)
# 2 = Divide resets state of current thread only
# (does not touch possible parasite threads)
+INJECT_METHOD 0 # 0 = Leaves the parasite thread state untouched.
+ # 1 = Resets the calling thread state on inject
GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
# increased on divide.
# 1 = Both the generation of the mother and child are
@@ -101,11 +122,16 @@
DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
+DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
+META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
+META_STD_DEV 0.0 # Standard deviation of meta mutation size.
+MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
+ # 2 = Mutation rates inherited from parent.
### REVERSION_GROUP ###
# Mutation Reversion
@@ -120,36 +146,56 @@
STERILIZE_BENEFICIAL 0.0 #
FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
# be eliminated?
-NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness to be considered neutral.
-NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness to be considered neutral.
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness
+ # to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness
+ # to be considered neutral.
### TIME_GROUP ###
# Time Slicing
-AVE_TIME_SLICE 30 # Ave number of insts per org per update
-SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
- # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
- # 2 = INTEGRATED: Perfectly integrated deterministic.
-BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
- # 1 = Merit proportional to copied size
- # 2 = Merit prop. to executed size
- # 3 = Merit prop. to full size
- # 4 = Merit prop. to min of executed or copied size
- # 5 = Merit prop. to sqrt of the minimum size
-BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
-DEFAULT_BONUS 1.0 # Initial bonus before any tasks
-MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
- # rather than the accumulated bonus of the parent?
-MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
-THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
- # (num_threads-1) * THREAD_SLICING_METHOD + 1
- # 0 = One thread executed per time slice.
- # 1 = All threads executed each time slice.
-MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
-DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
-DONATE_MULT 10.0 # Multiple of merit given that the target receives.
-MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
-MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
-MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
+ # 1 = Merit proportional to copied size
+ # 2 = Merit prop. to executed size
+ # 3 = Merit prop. to full size
+ # 4 = Merit prop. to min of executed or copied size
+ # 5 = Merit prop. to sqrt of the minimum size
+ # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
+ # rather than the accumulated bonus of the parent?
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
+ # (-1 = none, 0 = First in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
+ # per instruction (-1 = penalty, 0 = no effect.)
+FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
+ # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # (0 = off, 1 = on)
+FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 0 = One thread executed per time slice.
+ # 1 = All threads executed each time slice.
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
+MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
+MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
+ # donation attempt threshold; -1=no thresh
+DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+PRECALC_MERIT 0 # Pre-calculate merit at birth (unlimited resources only).
### GENEOLOGY_GROUP ###
# Geneology
@@ -214,3 +260,47 @@
MT_CONCURRENCY 1 # Number of concurrent analyze threads
ANALYZE_OPTION_1 # String variable accessible from analysis scripts
ANALYZE_OPTION_2 # String variable accessible from analysis scripts
+
+### ENERGY_GROUP ###
+# Energy Settings
+ENERGY_ENABLED 0 # Enable Energy Model. 0/1 (off/on)
+ENERGY_GIVEN_ON_INJECT 0 # Energy given to organism upon injection.
+ENERGY_GIVEN_AT_BIRTH 0 # Energy given to offspring upon birth.
+FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH 0.5 # Fraction of perent's energy given to offspring.
+FRAC_ENERGY_DECAY_AT_BIRTH 0.0 # Fraction of energy lost due to decay during reproduction.
+NUM_INST_EXC_BEFORE_0_ENERGY 0 # Number of instructions executed before energy is exhausted.
+ENERGY_CAP -1 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Int
+APPLY_ENERGY_METHOD 0 # When should rewarded energy be applied to current energy?
+ # 0 = on divide
+ # 1 = on completion of task
+ # 2 = on sleep
+ENERGY_VERBOSE 0 # Print energy and merit values. 0/1 (off/on)
+LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
+ # WARNING: may use lots of memory.
+
+### SECOND_PASS_GROUP ###
+# Tracking metrics known after the running experiment previously
+TRACK_CCLADES 0 # Enable tracking of coalescence clades
+TRACK_CCLADES_IDS coalescence.ids # File storing coalescence IDs
+
+### GX_GROUP ###
+# Gene Expression CPU Settings
+MAX_PROGRAMIDS 16 # Maximum number of programids an organism can create.
+MAX_PROGRAMID_AGE 2000 # Max number of CPU cycles a programid executes before it is removed.
+IMPLICIT_GENE_EXPRESSION 0 # Create executable programids from the genome without explicit allocation and copying?
+IMPLICIT_BG_PROMOTER_RATE 0.0 # Relative rate of non-promoter sites creating programids.
+IMPLICIT_TURNOVER_RATE 0.0 # Number of programids recycled per CPU cycle. 0 = OFF
+IMPLICIT_MAX_PROGRAMID_LENGTH 0 # Creation of an executable programid terminates after this many instructions. 0 = disabled
+IMPLICIT_REPRO_TIME 0 # Implicitly call the repro instruction after completing this many cpu cycles. 0 = disabled.
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
+PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
+PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
+ # instructions initiating execution (promoters are 1).
+REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
+REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
+ # Max regulation = 2^(REGULATION_STRENGTH/REGULATION_DECAY_FRAC)
Modified: development/tests/analyze_detail_all/test_list
===================================================================
--- development/tests/analyze_detail_all/test_list 2007-06-28 21:51:13 UTC (rev 1726)
+++ development/tests/analyze_detail_all/test_list 2007-06-29 16:47:05 UTC (rev 1727)
@@ -1,7 +1,7 @@
;--- Begin Test Configuration File (test_list) ---
[main]
; Command line arguments to pass to the application
-args =
+args = -s 100
app = %(default_app)s ; Application path to test
nonzeroexit = disallow ; Exit code handling (disallow, allow, or require)
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